Integrated Gene Analysis
| Gene Id | Log2Fc | Padj | Is Hub | Db Matched | Confidence | Tags |
|---|---|---|---|---|---|---|
| BRCA1 | -2.33 | 0.0005 | Yes | Yes | medium | HUB_GENE;PATHWAY_CENTRAL |
| PIK3CA | 2.08 | 0.05 | Yes | Yes | medium | HUB_GENE;PATHWAY_CENTRAL |
| MYC | -2.55 | 0.0059 | Yes | Yes | medium | HUB_GENE;PATHWAY_CENTRAL |
| BRAF | -2.38 | 0.0029 | No | Yes | medium | KNOWN_CANCER_GENE;PATHWAY_CENTRAL |
| ERBB2 | 2.54 | 0.02 | No | Yes | medium | KNOWN_CANCER_GENE;PATHWAY_CENTRAL |
| MET | -2.71 | 0.0076 | No | Yes | medium | KNOWN_CANCER_GENE;PATHWAY_CENTRAL |
| EGFR | 2.56 | 0.0071 | No | Yes | medium | KNOWN_CANCER_GENE;PATHWAY_CENTRAL |
| ROS1 | -2.80 | 0.02 | No | Yes | medium | KNOWN_CANCER_GENE;PATHWAY_CENTRAL |
| ALK | 2.62 | 0.0046 | No | Yes | medium | KNOWN_CANCER_GENE;PATHWAY_CENTRAL |
| KRAS | 2.38 | 0.04 | No | Yes | medium | KNOWN_CANCER_GENE;PATHWAY_CENTRAL |
| PTEN | 2.15 | 0.0065 | No | Yes | low | PATHWAY_CENTRAL |
| RB1 | 2.60 | 0.02 | No | Yes | low | PATHWAY_CENTRAL |
| BRCA2 | -1.99 | 0.0043 | No | Yes | low | PATHWAY_CENTRAL |
| APC | -2.71 | 0.0006 | No | Yes | low | PATHWAY_CENTRAL |
| CDK4 | -1.94 | 0.05 | No | Yes | low | PATHWAY_CENTRAL |
| CDKN2A | 1.79 | 0.0022 | No | Yes | low | PATHWAY_CENTRAL |
| TP53 | 2.17 | 0.0016 | No | Yes | low | PATHWAY_CENTRAL |
| GENE32 | 1.07 | 0.03 | Yes | No | novel_candidate | NOVEL_CANDIDATE;HUB_GENE |
| GENE48 | 1.49 | 0.0035 | Yes | No | novel_candidate | NOVEL_CANDIDATE;HUB_GENE |
| GENE18 | -1.91 | 0.02 | Yes | No | novel_candidate | NOVEL_CANDIDATE;HUB_GENE |
| GENE30 | 1.76 | 0.0082 | Yes | No | novel_candidate | NOVEL_CANDIDATE;HUB_GENE |
| GENE10 | 1.29 | 0.04 | Yes | No | novel_candidate | NOVEL_CANDIDATE;HUB_GENE |
| GENE31 | 1.58 | 0.0057 | Yes | No | novel_candidate | NOVEL_CANDIDATE;HUB_GENE |
| GENE55 | 1.45 | 0.0071 | Yes | No | novel_candidate | NOVEL_CANDIDATE;HUB_GENE |
| VEGFA | -1.46 | 0.0076 | No | No | requires_validation | TME_SIGNAL;PATHWAY_CENTRAL;REQUIRES_VALIDATION |
| GENE45 | 1.35 | 0.04 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE15 | 1.38 | 0.02 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE21 | -1.93 | 0.02 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE20 | -1.13 | 0.02 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE17 | 1.38 | 0.04 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE54 | -1.46 | 0.05 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE44 | 1.50 | 0.02 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE33 | 2.02 | 0.03 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE35 | -1.74 | 0.04 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE39 | -1.15 | 0.02 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE22 | -1.34 | 0.03 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE14 | 1.45 | 0.03 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE41 | -1.42 | 0.02 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE11 | -1.43 | 0.0076 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE13 | -1.28 | 0.02 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE56 | 1.38 | 0.0031 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE25 | 1.62 | 0.0006 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE53 | 1.70 | 0.0012 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE40 | 1.33 | 0.0016 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE42 | -1.56 | 0.0016 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE47 | 1.46 | 0.0016 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE50 | 1.46 | 0.0025 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE51 | 1.82 | 0.0026 | No | No | requires_validation | REQUIRES_VALIDATION |
| CTLA4 | 2.14 | 0.0029 | No | No | requires_validation | TME_SIGNAL;REQUIRES_VALIDATION |
| GENE24 | -1.67 | 0.0029 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE43 | -1.31 | 0.0033 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE26 | -1.22 | 0.02 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE58 | -1.82 | 0.0043 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE23 | 1.81 | 0.0043 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE27 | 1.66 | 0.0057 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE16 | 1.68 | 0.0059 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE59 | -1.38 | 0.0064 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE12 | 1.27 | 0.0006 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE38 | -1.36 | 0.0076 | No | No | requires_validation | REQUIRES_VALIDATION |
| GENE34 | 2.31 | 0.01 | No | No | requires_validation | REQUIRES_VALIDATION |
| CD274 | 2.16 | 0.01 | No | No | requires_validation | TME_SIGNAL;REQUIRES_VALIDATION |
| GENE49 | -1.35 | 0.05 | No | No | requires_validation | REQUIRES_VALIDATION |
Interpretation Results
Interpretation Guidelines Applied
- DEG alone does not equal biological importance
- DB match provides context, not proof
- DB mismatch means unknown, not unimportant
- Hub status increases confidence for novel candidates
- Pathway context strengthens interpretation
DB-Matched Genes
BRCA1
Confidence: medium
BRCA1 shows significant downregulated expression (log2FC=-2.33, padj<0.05). While BRCA1 is catalogued in cancer databases, it is not specifically associated with lung_cancer. Its role in this cancer type may warrant further investigation. Pathway analysis places BRCA1 in 17 enriched pathway(s), providing functional context for its potential role.
MYC
Confidence: medium
MYC shows significant downregulated expression (log2FC=-2.55, padj<0.05). While MYC is catalogued in cancer databases, it is not specifically associated with lung_cancer. Its role in this cancer type may warrant further investigation. Pathway analysis places MYC in 55 enriched pathway(s), providing functional context for its potential role.
PIK3CA
Confidence: medium
PIK3CA shows significant upregulated expression (log2FC=2.08, padj<0.05). While PIK3CA is catalogued in cancer databases, it is not specifically associated with lung_cancer. Its role in this cancer type may warrant further investigation. Pathway analysis places PIK3CA in 69 enriched pathway(s), providing functional context for its potential role.
BRAF
Confidence: medium
BRAF shows significant downregulated expression (log2FC=-2.38, padj<0.05). This gene is a known cancer gene specifically associated with lung_cancer, supporting its biological relevance in this context. Pathway analysis places BRAF in 47 enriched pathway(s), providing functional context for its potential role.
ALK
Confidence: medium
ALK shows significant upregulated expression (log2FC=2.62, padj<0.05). This gene is a known cancer gene specifically associated with lung_cancer, supporting its biological relevance in this context. Pathway analysis places ALK in 16 enriched pathway(s), providing functional context for its potential role.
EGFR
Confidence: medium
EGFR shows significant upregulated expression (log2FC=2.56, padj<0.05). This gene is a known cancer gene specifically associated with lung_cancer, supporting its biological relevance in this context. Pathway analysis places EGFR in 82 enriched pathway(s), providing functional context for its potential role.
MET
Confidence: medium
MET shows significant downregulated expression (log2FC=-2.71, padj<0.05). This gene is a known cancer gene specifically associated with lung_cancer, supporting its biological relevance in this context. Pathway analysis places MET in 31 enriched pathway(s), providing functional context for its potential role.
ERBB2
Confidence: medium
ERBB2 shows significant upregulated expression (log2FC=2.54, padj<0.05). This gene is a known cancer gene specifically associated with lung_cancer, supporting its biological relevance in this context. Pathway analysis places ERBB2 in 52 enriched pathway(s), providing functional context for its potential role.
ROS1
Confidence: medium
ROS1 shows significant downregulated expression (log2FC=-2.80, padj<0.05). This gene is a known cancer gene specifically associated with lung_cancer, supporting its biological relevance in this context. Pathway analysis places ROS1 in 14 enriched pathway(s), providing functional context for its potential role.
KRAS
Confidence: medium
KRAS shows significant upregulated expression (log2FC=2.38, padj<0.05). This gene is a known cancer gene specifically associated with lung_cancer, supporting its biological relevance in this context. Pathway analysis places KRAS in 70 enriched pathway(s), providing functional context for its potential role.
Novel Candidates
GENE48
Hypothesis: potential novel regulator
GENE48 shows significant upregulated expression (log2FC=1.49, padj<0.05). Although not in major cancer databases, GENE48 emerged as a hub gene (degree=1), suggesting potential regulatory importance. This may represent a novel candidate for this cancer type.
GENE31
Hypothesis: potential novel regulator
GENE31 shows significant upregulated expression (log2FC=1.58, padj<0.05). Although not in major cancer databases, GENE31 emerged as a hub gene (degree=1), suggesting potential regulatory importance. This may represent a novel candidate for this cancer type.
GENE55
Hypothesis: potential novel regulator
GENE55 shows significant upregulated expression (log2FC=1.45, padj<0.05). Although not in major cancer databases, GENE55 emerged as a hub gene (degree=1), suggesting potential regulatory importance. This may represent a novel candidate for this cancer type.
GENE30
Hypothesis: potential novel regulator
GENE30 shows significant upregulated expression (log2FC=1.76, padj<0.05). Although not in major cancer databases, GENE30 emerged as a hub gene (degree=1), suggesting potential regulatory importance. This may represent a novel candidate for this cancer type.
GENE18
Hypothesis: potential novel regulator
GENE18 shows significant downregulated expression (log2FC=-1.91, padj<0.05). Although not in major cancer databases, GENE18 emerged as a hub gene (degree=1), suggesting potential regulatory importance. This may represent a novel candidate for this cancer type.
GENE32
Hypothesis: potential novel regulator
GENE32 shows significant upregulated expression (log2FC=1.07, padj<0.05). Although not in major cancer databases, GENE32 emerged as a hub gene (degree=1), suggesting potential regulatory importance. This may represent a novel candidate for this cancer type.
GENE10
Hypothesis: potential novel regulator
GENE10 shows significant upregulated expression (log2FC=1.29, padj<0.05). Although not in major cancer databases, GENE10 emerged as a hub gene (degree=1), suggesting potential regulatory importance. This may represent a novel candidate for this cancer type.
VEGFA
Hypothesis: TME signal
VEGFA shows significant downregulated expression (log2FC=-1.46, padj<0.05). VEGFA is associated with tumor microenvironment signaling. Its expression change may reflect stromal or immune cell activity rather than tumor-intrinsic changes. Pathway analysis places VEGFA in 47 enriched pathway(s), providing functional context for its potential role.
GENE12
Hypothesis: requires functional validation
GENE12 shows significant upregulated expression (log2FC=1.27, padj<0.05). GENE12 is not catalogued in major cancer databases. Its significance remains to be determined through functional validation.
GENE25
Hypothesis: requires functional validation
GENE25 shows significant upregulated expression (log2FC=1.62, padj<0.05). GENE25 is not catalogued in major cancer databases. Its significance remains to be determined through functional validation.
Pathway Enrichment
| Database | Term Name | Padj | Gene Count |
|---|---|---|---|
| KEGG_2021_Human | Bladder cancer | 0.0000 | 10 |
| KEGG_2021_Human | Non-small cell lung cancer | 0.0000 | 11 |
| KEGG_2021_Human | Pancreatic cancer | 0.0000 | 11 |
| KEGG_2021_Human | Breast cancer | 0.0000 | 13 |
| KEGG_2021_Human | Melanoma | 0.0000 | 10 |
| GO_Molecular_Function_2023 | Transmembrane Receptor Protein Kinase Activity (GO:0019199) | 0.0005 | 4 |
| GO_Molecular_Function_2023 | Protein Tyrosine Kinase Activity (GO:0004713) | 0.0006 | 5 |
| GO_Molecular_Function_2023 | Transmembrane Receptor Protein Tyrosine Kinase Activity (GO:0004714) | 0.0006 | 4 |
| GO_Biological_Process_2023 | Positive Regulation Of Transferase Activity (GO:0051347) | 0.0011 | 6 |
| GO_Biological_Process_2023 | Regulation Of Cell Growth (GO:0001558) | 0.0011 | 7 |
| GO_Biological_Process_2023 | Regulation Of Kinase Activity (GO:0043549) | 0.0011 | 5 |
| GO_Biological_Process_2023 | Negative Regulation Of Cell Cycle (GO:0045786) | 0.0011 | 5 |
| GO_Biological_Process_2023 | Positive Regulation Of Phosphorylation (GO:0042327) | 0.0011 | 7 |
| GO_Molecular_Function_2023 | Protein Phosphatase Binding (GO:0019903) | 0.01 | 4 |
| GO_Molecular_Function_2023 | Ubiquitin Protein Ligase Binding (GO:0031625) | 0.03 | 5 |
Visualizations
Network Graph
Volcano Plot
Interpretation Summary
Pca Plot
Pathway Barplot
Heatmap Top50
Methods
Analysis Pipeline
- DEG Analysis: DESeq2 with |log2FC| > 1, padj < 0.05
- Network Analysis: NetworkX co-expression network, Spearman correlation > 0.7
- Pathway Enrichment: gseapy with GO (BP, MF, CC) and KEGG databases
- DB Validation: COSMIC Tier 1, OncoKB gene matching
- Interpretation: Systematic checklist-based scoring
Confidence Scoring
- Hub gene: +2 points
- DB matched: +2 points
- Cancer type specific: +1.5 points
- High pathway involvement: +0.5 points
Confidence Thresholds
- High: Score ≥ 5 and DB matched
- Medium: Score ≥ 3 and DB matched
- Novel Candidate: Not in DB but is Hub gene
- Requires Validation: Score < 1.5